Identify catalytic assignments in real chemical reaction networks

Determine, for specified non-equilibrium chemical reaction networks, which molecular species catalyze which reactions, enabling construction of accurate bipartite chemical reaction hypergraphs for testing the presence and properties of collectively autocatalytic sets.

Background

The theoretical analysis of autocatalytic sets often assumes a probabilistic assignment of catalysis due to incomplete knowledge of which molecules catalyze which reactions. This assumption leads to powerful predictions, including phase transitions to autocatalysis, but empirical mapping of catalyst-reaction relationships is necessary to refine models and validate predictions in actual chemical systems.

References

In general, we do not know which molecule catalyzes which reaction. In the absence of specific knowledge, theory and insight can proceed by the naïve assumption that each molecule has some probability, Pcat, to catalyze each reaction.

— Is the Emergence of Life an Expected Phase Transition in the Evolving Universe? (2401.09514 - Kauffman et al., 17 Jan 2024) in Part II, The Emergence of Molecular Reproduction as a First Order Phase Transition (following Figure 1b)